Initial support for tcrClustR

Author: bbimber

singlecell/resources/chunks/PerformTcrClustering.R

@@ -0,0 +1,23 @@
+for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+    seuratObj <- tcrClustR::CalculateTcrDistances(
+      inputData = seuratObj,
+      chains = c('TRA', 'TRB'),
+      minimumCloneSize = 2,
+      calculateChainPairs = TRUE
+    )
+
+    seuratObj <- tcrClustR::RunTcrClustering(
+      seuratObj_TCR = seuratObj,
+      dianaHeight = 20,
+      clusterSizeThreshold = 1
+    )
+
+    saveData(seuratObj, datasetId)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

singlecell/src/org/labkey/singlecell/SingleCellModule.java

@@ -29,7 +29,6 @@
 import org.labkey.api.singlecell.CellHashingService;
 import org.labkey.api.singlecell.pipeline.SingleCellRawDataStep;
 import org.labkey.api.singlecell.pipeline.SingleCellStep;
-import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.view.WebPartFactory;
 import org.labkey.singlecell.analysis.AbstractSingleCellHandler;
 import org.labkey.singlecell.analysis.CellRangerRawDataHandler;
@@ -76,6 +75,7 @@
 import org.labkey.singlecell.pipeline.singlecell.NormalizeAndScale;
 import org.labkey.singlecell.pipeline.singlecell.PerformDefaultNimbleAppend;
 import org.labkey.singlecell.pipeline.singlecell.PerformMhcDimRedux;
+import org.labkey.singlecell.pipeline.singlecell.PerformTcrClustering;
 import org.labkey.singlecell.pipeline.singlecell.PhenotypePlots;
 import org.labkey.singlecell.pipeline.singlecell.PlotAssayFeatures;
 import org.labkey.singlecell.pipeline.singlecell.PlotAverageCiteSeqCounts;
@@ -305,6 +305,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new CalculateTcrRepertoireStats.Provider());
         SequencePipelineService.get().registerPipelineStep(new PredictTcellActivation.Provider());
         SequencePipelineService.get().registerPipelineStep(new IdentifyAndStoreActiveClonotypes.Provider());
+        SequencePipelineService.get().registerPipelineStep(new PerformTcrClustering.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }

singlecell/src/org/labkey/singlecell/pipeline/singlecell/AbstractTcrClustRStep.java

@@ -0,0 +1,37 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider;
+import org.labkey.api.singlecell.pipeline.AbstractSingleCellPipelineStep;
+import org.labkey.api.util.PageFlowUtil;
+
+import java.util.Collection;
+
+abstract public class AbstractTcrClustRStep extends AbstractSingleCellPipelineStep
+{
+    public static String CONTAINER_NAME = "ghcr.io/bimberlabinternal/tcrclustr:latest";
+
+    public AbstractTcrClustRStep(PipelineStepProvider<?> provider, PipelineContext ctx)
+    {
+        super(provider, ctx);
+    }
+
+    @Override
+    public Collection<String> getRLibraries()
+    {
+        return PageFlowUtil.set("tcrClustR");
+    }
+
+    @Override
+    public String getDockerContainerName()
+    {
+        return CONTAINER_NAME;
+    }
+
+    // NOTE: ExperimentHub and similar packages default to saving data to the user's home dir. Set a directory, to avoid issues when not running the container as root
+    @Override
+    public String getDockerHomeDir()
+    {
+        return "/dockerHomeDir";
+    }
+}

singlecell/src/org/labkey/singlecell/pipeline/singlecell/PerformTcrClustering.java

@@ -0,0 +1,37 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SingleCellStep;
+
+import java.util.List;
+
+public class PerformTcrClustering extends AbstractTcrClustRStep
+{
+    public PerformTcrClustering(PipelineContext ctx, PerformTcrClustering.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("tcrClustR", "tcrClustR", "tcrClustR", "This will run tcrClustR to cluster TCRs by similarity.", List.of(
+
+            ), null, "https://github.com/bimberlabinternal/tcrClustR/");
+        }
+
+        @Override
+        public PerformTcrClustering create(PipelineContext ctx)
+        {
+            return new PerformTcrClustering(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "tcr";
+    }
+}